BMRBj - BMREntryMaster

Found 1 Document (0.562 seconds)

BMRB: 30259

5V0Y

Solution structure of arenicin-3.

Authors

Edwards, I.A., Mobli, M.

Assembly

arenicin-3

Entity

1. arenicin-3 (polymer), 21 monomers, 2617.066 Da Detail

GFCWYVCVYR NGVRVCYRRC N

Formula weight

2617.066 Da

Source organism

Arenicola marina

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.5 %, Completeness (bb): 78.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.5 % (206 of 256)	100.0 % (133 of 133)	51.5 % (51 of 99)	91.7 % (22 of 24)
Backbone	78.6 % (99 of 126)	100.0 % (44 of 44)	59.0 % (36 of 61)	90.5 % (19 of 21)
Sidechain	82.6 % (123 of 149)	100.0 % (89 of 89)	54.4 % (31 of 57)	100.0 % (3 of 3)
Aromatic	52.2 % (24 of 46)	100.0 % (23 of 23)	0.0 % (0 of 22)	100.0 % (1 of 1)
Methyl	93.8 % (15 of 16)	100.0 % (8 of 8)	87.5 % (7 of 8)

1. entity 1

GFCWYVCVYR NGVRVCYRRC N

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 3.3 (±0.05), Details 3.5 mM arenicin-3, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	arenicin-3	natural abundance		3.5 mM

Release date

2017-12-12

Citation

An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria
Elliott, A.G., Huang, J.X., Neve, S., Zuegg, J., Edwards, I.A., Cain, A.K., Boinett, C.J., Barquist, L., Lundberg, C.V., Steen, J., Butler, M.S., Mobli, M., Porter, K.M., Blaskovich, M., Lociuro, S., Strandh, M., Cooper, M.A.
Nat. Commun. (2020), 11, 3184-3184, PubMed 32576824 , DOI 10.1038/s41467-020-16950-x , Abstract

Related entities 1. arenicin-3, : 1 : 1 : 7 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30259_5v0y.nef
Input source #2: Coordindates	5v0y.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:3:CYS:SG	A:20:CYS:SG	oxidized, CA 55.813, CB 48.274 ppm	oxidized, CA 55.07, CB 48.781 ppm	2.002
A:7:CYS:SG	A:16:CYS:SG	oxidized, CA 55.136, CB 47.526 ppm	oxidized, CA 54.88, CB 48.492 ppm	1.978

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20-
GFCWYVCVYRNGVRVCYRRCN
|||||||||||||||||||||
GFCWYVCVYRNGVRVCYRRCN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0

Content subtype: combined_30259_5v0y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	206		100.0 (chain: A, length: 21)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	12 (1)	undefined	19.0 (chain: A, length: 21)
2	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	32 (1)	hbond	38.1 (chain: A, length: 21)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 132
  - ¹³C chemical shifts: 50
  - ¹⁵N chemical shifts: 24
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	132	99.2
¹³C chemical shifts	99	50	50.5
¹⁵N chemical shifts	28	24	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	43	97.7
¹³C chemical shifts	42	19	45.2
¹⁵N chemical shifts	21	18	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	89	100.0
¹³C chemical shifts	57	31	54.4
¹⁵N chemical shifts	7	6	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0
¹³C chemical shifts	8	7	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	23	100.0
¹³C chemical shifts	22	0	0.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 19.0%
- Total number of restraints: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: upper-bound-parabolic (12)
- Range of distance target values: 2.0, 3.1 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 38.1%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: upper-bound-parabolic (32)
  - Range of distance target values: 1.7, 3.2 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords ANTIMICROBIAL PROTEIN, antimicrobial peptide, b-hairpin

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.562 seconds)

BMRB: 30259

Sample

Related entities 1. arenicin-3, : 1 : 1 : 7 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail